{"files"=>["https://ndownloader.figshare.com/files/727037"], "description"=>"<p>The AP position of a threshold concentration of temporally-decreasing FGF8 results in a posterior-propagating determination front, anterior to which a cell becomes competent to sense the state of its intracellular segmentation clock. At the determination front, a cell determines its fated somitic cell type (core, anterior or posterior) based on the state of its segmentation clock. Differentiation follows four segmentation clock periods (corresponding to four somite lengths) later. The PSM grows continuously in the posterior direction through addition of cells from the tailbud, maintaining its length. <i>T</i><sub>clock</sub> is the period of the segmentation clock. (<i>Below</i>) The clock-wavefront interaction results in the spatial pattern of adhesion protein expression that creates the differential adhesion between somitic cell types assumed in our computational implementation of the clock-and-wavefront model: EphA4 occurs in the anterior compartment of the forming somite and the anterior of the PSM; ephrinB2 occurs in the posterior compartment of the forming somite; N-CAM occurs throughout the anterior of the PSM and in the somites; and N-cadherin is strong in the core of forming and formed somites.</p>", "links"=>[], "tags"=>["clock-and-wavefront", "relationships", "adhesion-protein"], "article_id"=>397388, "categories"=>["Biological Sciences", "Developmental Biology", "Biophysics"], "users"=>["Susan D. Hester", "Julio M. Belmonte", "J. Scott Gens", "Sherry G. Clendenon", "James A. Glazier"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1002155.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Schematic_A_typical_clock_and_wavefront_model_and_its_relationships_to_adhesion_protein_expression_/397388", "title"=>"Schematic: A typical clock-and-wavefront model and its relationships to adhesion-protein expression.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-10-06 02:03:08"}

{"files"=>["https://ndownloader.figshare.com/files/727678"], "description"=>"<p>(<b>A</b>–<b>C</b>) Lfng expression versus AP position and time for different segmentation-clock periods. (<b>A</b>) Increasing the segmentation-clock period to 180 min from the reference simulation period of 90 min decreases the spatial and temporal frequency of Lfng stripes compared to the reference simulation (<b>B</b>). (<b>C</b>) Decreasing the segmentation-clock period to 45 min increases the spatial and temporal frequency of Lfng stripes compared to the reference simulation ([Lfng] axis rescaled for clarity). (<b>D</b>) For a uniform Wnt3a concentration of 0.5 nM, <b>cells</b>' segmentation-clocks oscillate in phase with a period of 90 min. (<b>E</b>) Lfng concentration in a simulation with a segmentation-clock period of 45 min. The distance between the center and anterior (left) peaks is shorter than the distance between the center and posterior (right) peaks. Scale bar 40 µm. Parameters, when not otherwise noted, are equal to those in the reference simulation (<a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002155#pcbi-1002155-g007\" target=\"_blank\"><b>Figure 7</b></a>). The color scale is the same as that in <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002155#pcbi-1002155-g005\" target=\"_blank\"><b>Figure 5</b></a> (red indicates high concentration of Lfng and blue low concentrations of Lfng). We increase or decrease the segmentation-clock period by varying how long we integrate the segmentation-clock ODEs during each time step; by doing so, we easily vary the clock period relative to other processes in the simulation without altering parameters within the segmentation-clock submodel or changing the clock response to FGF8, Wnt3a or Delta/Notch signaling. For more information see <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002155#s3\" target=\"_blank\"><b>RESULTS</b></a><b>: Reference simulations reproduce key features of wild-type somitogenesis </b><b><i>in vivo</i></b>, <b>The number of high Lfng concentration stripes in the simulated PSM depends on the segmentation-clock period, PSM growth rate and PSM length</b> and <b>Somites form </b><b><i>in silico</i></b><b> in the absence of traveling gene expression stripes</b>.</p>", "links"=>[], "tags"=>["traveling", "lfng", "stripes", "segmentation-clock"], "article_id"=>398035, "categories"=>["Biological Sciences", "Developmental Biology", "Biophysics"], "users"=>["Susan D. Hester", "Julio M. Belmonte", "J. Scott Gens", "Sherry G. Clendenon", "James A. Glazier"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1002155.g008"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Anteriorly_traveling_Lfng_stripes_and_segmentation_clock_period_/398035", "title"=>"Anteriorly traveling Lfng stripes and segmentation-clock period.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-10-06 02:13:55"}

{"files"=>["https://ndownloader.figshare.com/files/728176"], "description"=>"<p><b>Ref</b> indicates the reference simulation, chosen because it most closely resembles somitogenesis <i>in vivo</i>.</p><p>Adhesion strength: “Weak” refers to the adhesion values for the determined cell types closer to the simulated PSM; “Strong” refers to the adhesion values for the determined cell types as shown in <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002155#pcbi-1002155-t003\" target=\"_blank\"><b>Table 3</b></a>.</p><p>Determination-differentiation mechanism: “Time delay” indicates that a cell-autonomous “ticker” was attached to each <b>cell</b> and counted down the interval between determination and differentiation; “FGF8 threshold” indicates that a second FGF8 threshold was set after determination, at which <b>cells</b> differentiated.</p><p>PSM cell motility: “Low” means λ<sub>surf</sub> = 25 and D<sub>cell</sub> = 0.86 µm<sup>2</sup>/min; “Reference” means λ<sub>surf</sub> = 15 and D<sub>cell</sub> = 1.08 µm<sup>2</sup>/min; and “High” means λ<sub>surf</sub> = 5 and D<sub>cell</sub> = 1.76 µm<sup>2</sup>/min.</p><p>Intersomitic gap formation: “Complete” means that every pair of somites in the simulation separated completely; “Good” means that somite boundaries are clear, but some <b>Core cells</b> persist in some intersomitic gaps; “% fused” gives the percentage by number of fused somites. See <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002155#pcbi-1002155-g010\" target=\"_blank\"><b>Figure 10</b></a> for clarification of the difference between fused somites and persistence of stranded <b>Core cells</b>.</p><p>Border correction: “N” means that cell sorting does not correct cell mixing across presumptive intersomitic borders; “Y” means that cell sorting corrects any cell mixing across presumptive intersomitic borders; “Some” means that cell sorting corrects some, but not all borders after cell mixing occurs.</p><p>Compartment borders: “Smooth” means that the populations of determined cell types are clearly separated with a smooth border between them; “Rough” means that the populations of determined cell types are separated, but the border between them is rough, with some cell mixing; “Very rough” means that the populations of determined cell types were not clearly separated and the border between them is fragmented due to cell mixing.</p><p>Traveling Lfng stripes: “Y” means that apparent traveling stripes of Lfng expression were observed in the simulation; “N” means that the traveling stripes were not observed.</p>", "links"=>[], "tags"=>["simulation"], "article_id"=>398534, "categories"=>["Biological Sciences", "Developmental Biology", "Biophysics"], "users"=>["Susan D. Hester", "Julio M. Belmonte", "J. Scott Gens", "Sherry G. Clendenon", "James A. Glazier"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1002155.t009"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Summary_of_simulation_results_for_different_mechanisms_/398534", "title"=>"Summary of simulation results for different mechanisms.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-10-06 02:22:14"}

{"files"=>["https://ndownloader.figshare.com/files/728451"], "description"=>"<p>“Reference” indicates that the value is the same as in the reference simulation; “Variable” indicates that the value is free to change in response to changes in other factors; “High” and “Low” indicate imposed changes; “Increased” and “Decreased” indicate results for imposed changes. All are relative to the values in the reference simulation.</p><p>For more information see <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002155#s3\" target=\"_blank\"><b>RESULTS</b></a><b>: The number of high Lfng concentration stripes in the simulated PSM depends on the segmentation-clock period, PSM growth rate and PSM length</b>.</p>", "links"=>[], "tags"=>["lfng", "stripes", "modeled", "segmentation-clock"], "article_id"=>398806, "categories"=>["Biological Sciences", "Developmental Biology", "Biophysics"], "users"=>["Susan D. Hester", "Julio M. Belmonte", "J. Scott Gens", "Sherry G. Clendenon", "James A. Glazier"], "doi"=>["https://dx.doi.org/10.1371/journal.pcbi.1002155.t007"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Dependence_of_the_number_of_Lfng_stripes_in_the_modeled_PSM_on_the_PSM_growth_rate_and_segmentation_clock_period_/398806", "title"=>"Dependence of the number of Lfng stripes in the modeled <b>PSM</b> on the <b>PSM</b> growth rate and segmentation-clock period.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-10-06 02:26:46"}